I don't think it matters too much which way you choose to water so long as:
1. When watering the "standard way" by pouring water in through the top you do it long enough to make sure everything is thoroughly wet.
2. When soaking you don't leave them standing in water for too long (I make sure not to leave mine in for more than an hour, but they shouldn't need any more than 15 min). Also make sure to soak them separately and not re-use the water so as to not spread any potential disease/bugs from one pot to another.
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